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United States Department of Agriculture

Agricultural Research Service

Molecular Plant Pathology
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The Molecular Plant Pathology (MPP) program is assigned to identify the genetic and pathological tools and resources for rice breeding.  Currently, rice blast disease caused by the ascomycete fungus Magnaporthe oryzae, and sheath blight disease caused by the necrotrophic soil-borne pathogen Rhizoctonia solaniare the two major destructive fungal diseases worldwide (Fig. 1 & 2). Both rice blast and sheath blight diseases in the U.S. have been managed using genetic resistance (major and minor genes) integrated with cultural practices. However, continued evolution and adaptation of the pathogen have been challenging the effectiveness of deployed resistance genes in commercial cultivars. The current focus of the MPP program is to study rice - M. oryzae, and rice - R. solani pathosystems, and to apply molecular techniques to identify sources of disease resistance, and to design strategies to accelerate incorporation of resistance genes into improved germplasm.


Figure 1




Figure 2




Specific objectives:

  • To examine the co-evolution of the blast resistance gene Pi-tain rice with the corresponding avirulence gene AVR-Pitain M. oryzaefor developing novel disease management strategies (partially supported by the National Science Foundation-Weedy Rice Project)

  • To identify the interaction components in the Pi-ta gene-mediated signal recognition and transduction pathways  for developing durable resistance strategies
  • To analyze structural and functional relationships of AVR-Pita  for predicting the stability of blast resistance in current cultivars (partially supported by the University of Arkansas Rice Research and Promotion Board)
  • To identify differentially and highly expressed genes after rice is infected either with the rice blast fungus or sheath blight fungus to develop molecular strategies that will improve resistance in enhanced rice germplasm (partially supported by USDA-CSREES RiceCAPproject)
  • To develop useful genetic stocks and mapping populations for mapping and cloning resistance genes to both rice blast and sheath blight diseases (GSOR Collection Catalog)
  • To develop a large deletion mutant population for functional genomic studies and rice improvement (GSOR Collection Catalog)
  • To develop and improve tools for genetics and pathology
  • To monitor the disease epidemics and study the mechanisms of pathogenesis
  • To study mechanisms of fissuring for developing new knowledge for breeders to use for improving milling quality (partially supported by USA Rice Foundation)
  • To understand mechanisms of rice epigenetics for improving yield potential and stress resistance (partially supported by the National Science Foundation)

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Project Personnel:


Yulin Jia - Research Plant Molecular Pathologist - Scientist


NSF PROJECT (award IOS-1032023):  Genomic Structure and Contemporary Evolution of Weediness in Red Rice



Dr. Yan Liu is a Postdoctoral Research Associate of University of Arkansas Rice Research and Extension who is conducting research on evolutionary genomics of invasive species of rice, a project funded by National Science Foundation.  Her responsibilities include phenotyping and genotyping of weedy traits of invasive species of rice in laboratory, greenhouse and field.  Please visit this site for additional information on the project:


Michael J. Lin - Biological Science Lab Technician



Responsibilities include: 1) manage greenhouse to provide rice plants for the MPP program, 2) develop rice mapping population and 3) to evaluate disease reactions for different projects to study the genetic interaction between rice and pathogens.



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Tracy Bianco is a Biological Science Lab Technician.  Her responsibility includes, but is not limited to, lab management to provide stock solutions, chemicals and supplies for the MPP program, fungal and plant DNA, RNA and protein storage, preparation, and analysis. 

 Rabie AS Elshafey  

Dr. Rabie AS Elshafey is a senior Research Plant Pathologist from the Rice Research and Training Center in Egypt.  He is participating in a team investigation on rice blast and false smut disease management at the Dale Bumpers National Rice Research Center through the University of Arkansas. 


Carson Kleinbeck was hired as a part-time Research Aid.  Carson is attending Stuttgart High School.  He loves math and science.  His responsibility is to assist genetic studies of rice genes that are responsible for the weedy phenotype.  This project is funded by the National Science Foundation through the University of Arkansas Rice Research and Extension Center.



Alan Sites is a student of the University of Arkansas at Fayetteville.  His responsibilities include, but are not limited to, growing and evaluating plants after treatments with stress in greenhouses and fields.

Alan Sites




Ms. Xue Jin is a Research Assistant funded by a grant from the Arkansas Rice Research and Promotion Board.  Her responsibility includes, but is not limited to, fungal culture, single spore isolation and storage, disease inoculation, and DNA analysis.


Jianbing Ma is involved in team investigation on genetic analysis of rice genes involved in disease resistance and productivity.  His visit is funded by a grant from the National Science Foundation through the University of Arkansas Rice Research and Extension Center.


Md. Mamunur Rasheed is a Professional Assistant of the University of Arkansas Rice Research and Extension Center who is performing research on rice panicle blight at the USDA-ARS Dale Bumpers National Rice Research Center. This project is funded by the UA Arkansas Rice Research and Promotion Board.


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Research Snapshots:

 Please click here to see posters from the 2010 Rice Field Day held August 11 at the University of Arkansas Rice Research and Extension Center and the 5th International Rice Blast Conference held August 11-14 in Little Rock, Arkansas.

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Last Modified: 9/26/2013
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